Package 'scOntoMatch'

make sure ontology names are all translated to ontology ids while warning, consider manual reannotation

Description

make sure ontology names are all translated to ontology ids while warning, consider manual reannotation

Usage

check_ontology_translate(obj, onts, ont, anno_col)

Arguments

obj	seurat rds object
onts	ontology ids from translate
ont	ontologyIndex object
anno_col	annotation column in [email protected] that is translated to onts ids

Value

do not return a value but output messages

---

Get a names list of ontology and id by id

Description

Get a names list of ontology and id by id

Usage

fill_query(all, query)

Arguments

all	all ontology id to plot tree
query	query ontology id to fill

Value

a color object to fill query in onto_plot

Examples

## Not run: 
fill_query(all = c("CL0000548", "CL:0000066", "CL:0000082"), query = c("CL:0000082"))

## End(Not run)

---

Get a names list of ontology and id by name

Description

Get a names list of ontology and id by name

Usage

getOntologyId(ont, onto_name)

Arguments

ont	ontology object
onto_name	character vector of ontology names

Value

a named list mapping ontology id and ontology name

Examples

## Not run: 
getOntologyId(onto_name = "epithelial cell of lung", ont = ont)

## End(Not run)

---

Get a names list of ontology and id by id

Description

Get a names list of ontology and id by id

Usage

getOntologyName(ont, onto_id)

Arguments

ont	ontology object
onto_id	character vector of ontology ids

Value

a named list mapping ontology id and ontology name

Examples

## Not run: 
getOntologyName(onto_id = "epithelial cell of lung", ont = ont)

## End(Not run)

---

match ontology terms by direct mapping and mapping descendants to ancestors

Description

match ontology terms by direct mapping and mapping descendants to ancestors

Usage

getOntoMapping(ont, onts1, onts2)

Arguments

ont	the ontology object from get_OBO
onts1	a character vector of ontology id
onts2	a character vector of ontology id

Value

a named list for ontology id mapping looks like ontology_id:ontology_id

Examples

## Not run: 
getOntoMapping(ont = ont, onts1 = "CL:0000548", onts2 = c("CL0000548", "CL:0000066"))

## End(Not run)

---

match descendant terms to ancestor terms within a dataset

Description

match descendant terms to ancestor terms within a dataset

Usage

getOntoMinimal(ont, onts)

Arguments

ont	the ontology object from get_OBO
onts	a character vector of ontology id

Value

a named list for ontology id mapping looks like ontology_id:ontology_id

Examples

## Not run: 
getOntoMinimal(ont = ont, onts = c("CL0000548", "CL:0000066", "CL:0000082"))

## End(Not run)

---

Match descendants to ancestors in multiple ontology id lists

Description

Match descendants to ancestors in multiple ontology id lists

Usage

getOntoMultiMapping(ont, onts)

Arguments

ont	ontologyIndex object
onts	named list of ontology ids

Value

a named character of mapping from:mapping to

Examples

## Not run: 
getOntoMultiMapping(ont = ont, onts = c("CL0000548", "CL:0000066", "CL:0000082"))

## End(Not run)

---

read in seurat object .rds files as a named list of seurat object

Description

read in seurat object .rds files as a named list of seurat object

Usage

getSeuratRds(metadata, sep)

Arguments

metadata	a metadata file indicating name, path to 'seurat' rds file
sep	sep of the metadata file

Value

a named list contains data name and the corresponding 'seurat' object

Examples

## Not run: 
getSeuratRds(metadata = 'metadata.tsv', sep = '\t')

## End(Not run)

---

get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Description

get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Usage

ontoMinimal(obj, ont, anno_col, onto_id_col)

Arguments

obj	the seurat object
ont	ontologyIndex object
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping

Value

an seurat object with meta.data[["cell_ontology_base"]]

Examples

## Not run: 
ontoMinimal(obj = seurat_obj, ont = ont, anno_col = 'ontology_name', onto_id_col = 'ontology_id')

## End(Not run)

---

Core function of scOntoMatch Match the ontology annotation of multiple seurat objects

Description

Core function of scOntoMatch Match the ontology annotation of multiple seurat objects

Usage

ontoMultiMatch(obj_list, anno_col, onto_id_col, ont)

Arguments

obj_list	a namesd list of seurat objects to match
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping
ont	ontologyIndex object

Value

a list of seurat objects with annotation ontology mapped to each-other in obs[['cell_ontology_mapped']]

Examples

## Not run: 
ontoMultiMatch(seurat_obj_list, ont, "ontology_name", 'ontology_id')

## End(Not run)

---

get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Description

get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation

Usage

ontoMultiMinimal(obj_list, ont, anno_col = "cell_ontology_base", onto_id_col)

Arguments

obj_list	a named list of seurat objects
ont	ontologyIndex object
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping

Value

a named list of seurat objects with meta.data[["cell_ontology_base"]]

Examples

## Not run: 
ontoMultiMinimal(seurat_obj_list, ont, "cell_ontology_base", 'ontology_id')

## End(Not run)

---

translate named list of obj_list to named list of cell ontology ids per obj

Description

translate named list of obj_list to named list of cell ontology ids per obj

Usage

ontoTranslate(obj_list, ont, onto_id_col, anno_col)

Arguments

obj_list	a named list of seurat object
ont	ontologyIndex object
onto_id_col	if also have ontology id column for direct mapping
anno_col	the cell ontology text annotation column name

Value

a named list of cell ontology ids

Examples

## Not run: 
ontoTranslate(seurat_obj_list, ont, 'ontology_name', 'ontology_id')

## End(Not run)

---

Plot a ontology tree with matched ontology from ontoMatch

Description

Plot a ontology tree with matched ontology from ontoMatch

Usage

plotMatchedOntoTree(
  obj_list,
  ont,
  anno_col = "cell_ontology_mapped",
  onto_id_col,
  roots = c("CL:0000548"),
  ...
)

Arguments

obj_list	a list of seurat obj files as the output of ontoMatch
ont	ontology object
anno_col	the cell ontology text annotation column name
onto_id_col	if also have ontology id column for direct mapping
roots	root ontology in tree to plot, default "animal cells" in cell ontology
...	additional parameters for ontologyPlot::onto_plot

Value

a lit of matched ontology tree plot

Examples

## Not run: 
plotMatchedOntoTree(seurat_obj_list, ont, 'cell_ontology_mapped', 'ontology_id')

## End(Not run)

---

Plot a tree representation of ontology terms

Description

Plot a tree representation of ontology terms

Usage

plotOntoTree(
  ont,
  onts,
  plot_ancestors = TRUE,
  ont_query = NULL,
  roots = c("CL:0000548"),
  ...
)

Arguments

ont	ontology object
onts	ontology ids to plot
plot_ancestors	if plot ancestors or not
ont_query	query ontology to highlight in the tree
roots	root ontology in tree, default "animal cells" in cell ontology
...	additional parameters for ontologyPlot::onto_plot

Value

an ontology tree plot

Examples

## Not run: 
plotOntoTree(ont = ont, onts = c("CL:0000066", "CL:0000082"), ont_query = c("CL:0000082"))

## End(Not run)

---